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//******************************************************************************
//
// File: AlignmentStats.java
// Package: edu.rit.compbio.seq
// Unit: Interface edu.rit.compbio.seq.AlignmentStats
//
// This Java source file is copyright (C) 2008 by Alan Kaminsky. All rights
// reserved. For further information, contact the author, Alan Kaminsky, at
// ark@cs.rit.edu.
//
// This Java source file is part of the Parallel Java Library ("PJ"). PJ is free
// software; you can redistribute it and/or modify it under the terms of the GNU
// General Public License as published by the Free Software Foundation; either
// version 3 of the License, or (at your option) any later version.
//
// PJ is distributed in the hope that it will be useful, but WITHOUT ANY
// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
// A PARTICULAR PURPOSE. See the GNU General Public License for more details.
//
// Linking this library statically or dynamically with other modules is making a
// combined work based on this library. Thus, the terms and conditions of the
// GNU General Public License cover the whole combination.
//
// As a special exception, the copyright holders of this library give you
// permission to link this library with independent modules to produce an
// executable, regardless of the license terms of these independent modules, and
// to copy and distribute the resulting executable under terms of your choice,
// provided that you also meet, for each linked independent module, the terms
// and conditions of the license of that module. An independent module is a
// module which is not derived from or based on this library. If you modify this
// library, you may extend this exception to your version of the library, but
// you are not obligated to do so. If you do not wish to do so, delete this
// exception statement from your version.
//
// A copy of the GNU General Public License is provided in the file gpl.txt. You
// may also obtain a copy of the GNU General Public License on the World Wide
// Web at http://www.gnu.org/licenses/gpl.html.
//
//******************************************************************************
package edu.rit.compbio.seq;
import java.io.PrintStream;
/**
* Interface AlignmentStats specifies the interface for an object that computes
* statistics of an {@linkplain Alignment}. Methods are provided to compute the
* raw score, the bit score, and the <I>E</I>-value. The formulas for these
* statistics depend on the procedure used to produce the alignment.
*
* @author Alan Kaminsky
* @version 01-Jul-2008
*/
public interface AlignmentStats
{
// Exported operations.
/**
* Returns the raw score for the given alignment. A larger raw score
* signifies a greater degree of similarity between the query sequence and
* subject sequence that were aligned.
*
* @param alignment Alignment.
*
* @return Raw score.
*/
public double rawScore
(Alignment alignment);
/**
* Returns the bit score for the given alignment. A larger bit score
* signifies a greater degree of similarity between the query sequence and
* subject sequence that were aligned.
* <P>
* The bit score is the raw score normalized to units of "bits." Bit scores
* for different alignment procedures may be compared, whereas raw
* (unnormalized) scores for different alignment procedures may not be
* compared.
*
* @param alignment Alignment.
*
* @return Bit score.
*/
public double bitScore
(Alignment alignment);
/**
* Returns the <I>E</I>-value (expect value) for the given alignment. A
* smaller <I>E</I>-value signifies a more statistically significant degree
* of similarity between the query sequence and subject sequence that were
* aligned.
* <P>
* The <I>E</I>-value is the expected number of alignments with a score
* greater than or equal to the <TT>alignment</TT>'s score when a
* randomly-chosen query of the same length as the query that produced the
* <TT>alignment</TT> is matched against the database.
*
* @param alignment Alignment.
*
* @return Bit score.
*/
public double eValue
(Alignment alignment);
/**
* Print information about this alignment statistics object on the given
* print stream.
*
* @param out Print stream.
*/
public void print
(PrintStream out);
}
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